matsengrp cft issues - Githubissues

matsengrp / cft

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Introduction on the program

#312 xuanmingshi closed 2 years ago
1
Use new partis fcn add_seqs_to_line()

#311 psathyrella opened 4 years ago
6
Validate parsing of partis multiplicity

#310 eharkins closed 4 years ago
15
286 indel trees

#309 eharkins closed 4 years ago
0
Nextflow

#308 eharkins opened 4 years ago
0
update partis selection metrics

#307 eharkins closed 4 years ago
0
Preserve ambiguous nucleotides

#306 eharkins closed 4 years ago
1
Update partis selection metrics

#305 eharkins closed 4 years ago
0
update partis get-selection-metrics/get-tree-metrics call

#304 psathyrella closed 4 years ago
1
environment.yml

#303 eharkins closed 4 years ago
0
170 raxml-ng

#302 eharkins closed 4 years ago
0
299 cleanup

#301 eharkins closed 4 years ago
0
partis utils.restrict_to_iseqs change

#300 eharkins closed 4 years ago
0
Remove commented out / unused code and run code formatter

#299 eharkins closed 4 years ago
0
update testing framework

#298 eharkins opened 4 years ago
1
295 downsampling large clusters

#297 eharkins closed 4 years ago
0
186 blast for observed ancestors

#296 eharkins closed 4 years ago
0
Reconsider subsampling/pruning procedure

#295 eharkins closed 4 years ago
19
Flow chart defining correspondence between Overbaugh and Matsen teams on B-cell research

#294 eharkins closed 4 years ago
11
Output full partis cluster fasta

#293 eharkins closed 4 years ago
2
274 alignment

#292 eharkins closed 4 years ago
2
276 linearham integration

#291 eharkins closed 4 years ago
0
Check whether naive was sampled

#290 eharkins closed 4 years ago
1
273 process all part steps

#289 eharkins closed 5 years ago
1
Track build options alongside input data

#288 eharkins opened 5 years ago
1
Archiving data for manuscripts

#287 lauradoepker closed 4 years ago
6
Add indel tree analysis to pipeline?

#286 eharkins closed 4 years ago
9
Resolve insertion in QA255.016-VL

#285 eharkins closed 4 years ago
2
281 process seed indels

#284 eharkins closed 5 years ago
0
Olmsted frozen deployments

#283 matsen closed 5 years ago
4
Make it very obvious when sequences have an indel

#282 matsen closed 5 years ago
7
Add process_partis.py option for a specific indel

#281 eharkins closed 5 years ago
6
improve view-output output

#280 psathyrella closed 5 years ago
1
Investigate shm indel in QA255.157-Vk

#279 psathyrella closed 5 years ago
10
Can we use synthetic spike-ins?

#278 psathyrella opened 5 years ago
0
Indel handling in QA255.157-Vk

#277 lauradoepker closed 5 years ago
9
Bayesian analysis integration

#276 matsen opened 5 years ago
11
clean up glfo treatment

#275 psathyrella closed 5 years ago
0
Remove cft alignment step

#274 psathyrella opened 5 years ago
15
Do not process partis non-"best" partitions by default

#273 eharkins closed 5 years ago
17
Use partis tree metrics script without calling annotate

#272 eharkins closed 5 years ago
0
263 n total reads

#271 eharkins closed 5 years ago
1
266 partis alt naive analysis

#270 eharkins closed 5 years ago
1
268 timepoint reqs

#269 eharkins closed 5 years ago
1
Stricter requirements for timepoint data

#268 eharkins closed 5 years ago
4
Rename things to match olmsted terminology

#267 metasoarous opened 5 years ago
0
Create logo plot from partis alternative naives

#266 eharkins closed 5 years ago
4
264 annotation index

#265 eharkins closed 5 years ago
6
Fix unchecked index in merge_selection_metrics.py

#264 eharkins closed 5 years ago
5
Add version of `n_seqs` summing over multiplicity data

#263 metasoarous closed 5 years ago
18